miLineage-package: Association Tests for Microbial Lineages on a Taxonomic Tree
In miLineage: Association Tests for Microbial Lineages on a Taxonomic Tree

Description Details Author(s) References Examples

A variety of association tests for microbiome data analysis described in Tang Z.-Z. et al.(2017) <doi: 10.1093/bioinformatics/btw804> and Tang Z.-Z. & Chen G. (2017) <Submitted>. miLineage allows users to (a) perform tests on multivariate taxon counts; (b) localize the covariate-associated lineages on the taxonomic tree; and (c) assess the overall association of the microbial community with the covariate of interest.

Package:	miLineage
Type:	Package
Version:	2.1
Date:	2018-03-09
License:	GPL (>=2)

QCAT, QCAT_GEE, ZIGDM

Zheng-Zheng Tang

Maintainer: Zheng-Zheng Tang <tang@biostat.wisc.edu>

1. Tang, Z.-Z., Chen, G., Alekseyenko, A. V., and Li, H. (2017). A General Framework for Association Analysis of Microbial Communities on a Taxonomic Tree. Bioinformatics, 33(9), 1278-1285.
2. Tang, Z.-Z. and Chen, G. (2017). Zero-Inflated Generalized Dirichlet Multinomial Regression Model for Microbiome Compositional Data Analysis. Submitted.

data(data.toy)
OTU.toy = data.toy$OTU.toy
Tax.toy = data.toy$Tax.toy
case = data.toy$covariate.toy
# the OTUs should be consistent between the OTU table and the taxonomy table
OTU.toy.reorder = OTU.toy[,match(rownames(Tax.toy), colnames(OTU.toy))]
# perform QCAT test for detecting differential mean
QCAT(OTU.toy.reorder, case, 1, Tax.toy, fdr.alpha=0.05)
# perform ZIGDM test for detecting differential dispersion
ZIGDM(OTU.toy.reorder, NULL, NULL, case, test.type = "Disp", 1, 
  ZI.LB = 10, Tax.toy, fdr.alpha = 0.05)